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Reads Filtering Specifications

Process Details

  • Name: readsFiltering
  • Process UUID: be44d212da5a472c82569dceb5021698
  • Process Group: uminator

Overview

This process performs quality filtering on nanopore sequencing reads to remove low-quality sequences and reads outside specified length ranges. The filtering is optional and can be bypassed while maintaining consistent output structure.

This process is implemented in Bash, which invokes NanoFilt for quality and length-based filtering of nanopore reads.

Key Functionality

  • Quality Filtering: Removes reads below a specified quality threshold using NanoFilt
  • Length Filtering: Filters reads based on minimum and maximum length criteria
  • Optional Processing: Allows bypassing of filtering while maintaining output directory structure
  • Compressed Input Handling: Processes gzipped FASTQ files directly without decompression

Input/Output Specification

Inputs

Required Inputs

  • reads

    • Description: Nanopore sequencing reads in FASTQ format
    • Format: FASTQ (compressed or uncompressed)

  • mate

    • Description: Sample identifier for organizing output files
    • Format: String value

Outputs

  • outputDir
    • Description: Directory containing filtered reads with sample-specific subdirectories
    • Format: Directory structure

References & Resources

  • Tool Documentation: NanoFilt is part of the NanoStat/NanoPlot suite for nanopore data analysis